3EG5

Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z2CPDB ENTRY 1Z2C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.8293Bis-Tris-Propane (PH 8.8 adjusted with citric acid), 26% (w/v) PEG 3350, 250mM Na-Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8156.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.269α = 90
b = 71.269β = 90
c = 244.964γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2007-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9763SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.743.47899.50.0740.08413.523.23824138038
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.899.80.3810.3333.693.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Z2C2.743.473803836130190899.490.208160.206290.24333RANDOM53.029
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.190.090.19-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.536
r_dihedral_angle_3_deg17.867
r_dihedral_angle_4_deg15.034
r_dihedral_angle_1_deg5.023
r_scangle_it1.411
r_angle_refined_deg1.104
r_scbond_it0.828
r_mcangle_it0.598
r_mcbond_it0.347
r_symmetry_hbond_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.536
r_dihedral_angle_3_deg17.867
r_dihedral_angle_4_deg15.034
r_dihedral_angle_1_deg5.023
r_scangle_it1.411
r_angle_refined_deg1.104
r_scbond_it0.828
r_mcangle_it0.598
r_mcbond_it0.347
r_symmetry_hbond_refined0.333
r_nbtor_refined0.298
r_nbd_refined0.203
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.143
r_chiral_restr0.072
r_metal_ion_refined0.068
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8228
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms66

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling